Abstract

MOTIVATION: The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those data sets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. RESULTS: We restructure the GRM estimation phase of the code and introduce the highly optimized parallel BLAS library combined with manual parallelization and optimization. We introduce the LAPACK library into the REML analysis stage. For a testcase with 8999 individuals and 279,435 SNPs we reduce the total runtime, using a compute node with 2 multi-core Intel Nehalem CPUs, from around 17 hours to around 11 minutes. AVAILABILITY: The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta. CONTACT: a.gray@ed.ac.uk.